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PubMed2026

Large-scale simulation of coverage and error rate tradeoffs for cancer detection in cell-free DNA whole-genome sequencing.

MOTIVATION: Cell-free DNA (cfDNA) whole-genome sequencing (WGS) is a promising approach for detecting cancer recurrence. It enables cancer detection by identifying all tumor-derived cfDNA (ctDNA) molecules carrying somatic single nucleotide variants (sSNVs). While ideally, a sequencing platform should be highly accurate for reliable ctDNA detection, in reality, all sequencing platforms introduce sequencing errors that generate false positives indistinguishable from true SNVs. Understanding how sequencing parameters influence ctDNA detection sensitivity at low tumor fractions (TFs) in cfDNA samples is essential for guiding sequencing strategies in clinical contexts. To model cfDNA sequencing for tumor detection, which contains asymmetric noise and multiple interacting parameters, analytical modeling is intractable, motivating large-scale parallelized simulation. RESULTS: We developed a simulation framework to generate in silico cfDNA data across 10 cancer types. In total, 480 million cfDNA samples were simulated from tumor WGS profiles. Overall, the lowest detectable TF differs substantially between cancer types under identical sequencing conditions due to variations in mutational load. For cancers with high mutational load, 3× coverage with low-error techniques reliably detects TFs below 0.1%. In contrast, cancers with low mutational load require at least six-fold higher coverage to achieve comparable detection thresholds. Increasing sequencing quality scores from Q30 to Q55 at 30× coverage further enhances sensitivity, enabling detection of TFs as low as 1 × 10-5. This study provides a comprehensive framework for optimizing sequencing parameters, offering valuable guidance for tailoring future technology development for specific cancer types and clinical applications. AVAILABILITY AND IMPLEMENTATION: The code is publicly available at https://github.com/UMCUGenetics/cfdetect/tree/main.

Whole Genome Sequencing↗

PubMed2003

A phylogenetic approach to assessing the significance of missense mutations in disease genes.

The identification of deleterious mutations within candidate genes is a crucial step in the elucidation of the genetic bases of human disease. However, the significance of any base or amino acid change within a gene is unknown until detailed structural and functional analysis has been carried out. A potentially rapid way of identifying functionally important sites within a gene is to identify evolutionarily conserved regions. Mutations affecting such sites are assumed to be deleterious for the carrier. In this communication we generalize this approach and present a formal framework to assess whether a specific mutation is deleterious given sequence data from a set of homologues. We propose a score that takes into account the nature of the mutation, the conservation of the affected residue among the different species, and their phylogenetic relationships. Its performance is examined using published TP53 mutations and frequent polymorphic variants.

Computational Biology↗

PubMed1993

Age differences in memory-span errors: speed or inhibitory mechanisms?

This study investigated age differences in errors on the digit-span task. Protocols of 119 men and women, aged 18-99 years, were scored for the occurrence of three types of errors derived from the speed-of-processing and inhibition-deficit frameworks: omission errors, intrusion errors, and transposition errors. The types of errors made on the digit-span task varied with span size. At larger span sizes, participants were more likely to omit digits or introduce nonstimulus digits than to transpose those in storage. No age differences in intrusion errors were found, however, old-old women (75+ years) were significantly more likely than young (18-25 years) and old (60-70 years) adults of either sex to exhibit transposition errors. Consequently, old-old women were significantly less likely to exhibit omission errors. The results indicate that the digit-span task may involve two parallel processes: digit storage/recall and serial/position storage-recall. Age differences in the serial-processing component, rather than in the digit storage/recall component, may be age sensitive. These results are discussed within an inhibition-deficit framework of cognitive aging.

Adolescent↗

PubMed1984

The permanence of otoplasty in the rabbit ear: a comparison of techniques.

Otoplasty should restructure the cartilage framework of the ear with permanent results. Major techniques include the placement of permanent sutures, with or without concomitant cartilage scoring, and cartilage abrasion alone. Our study evaluates the durability of the results of each method. Fifteen New Zealand white rabbits were divided into two groups. In 10 rabbits, the posterior surface of the right ear cartilage was abraded, and the ear was folded forward and secured with nylon stitches. A similar procedure was performed on the left ear, omitting the cartilage abrasion. In 4 rabbits, both ears were abraded transversely on the posterior cartilaginous surface and no sutures were placed. In 1 rabbit only the posterior skin was undermined on both ears. For one week dressings maintained a right-angle fold at the operative site. Rabbit ears reshaped with abrasion only failed to maintain the desired conformation. Ears with suture and abrasion did not maintain the full 90-degree angle created at surgery, although they did not fully straighten. Ears reshaped with suture alone maintained a folded angle close to the original right angle. Three months after operation the sutures within the cartilage were removed to approximate the clinical situation of late suture disruption from trauma to the operated ear and the shape was assessed.

Animals↗

PubMed2001

Validity evidence for using a general critical thinking test to measure nursing students' critical thinking.

This study examined validity evidence for using a general test of critical-thinking skills and dispositions to measure nursing students' critical-thinking abilities. Content evidence indicated strong support for the theoretical framework underlying the test but less support for the way in which the critical-thinking constructs were specifically measured. Scores related to critical-thinking skills demonstrated significant but low correlations with grade point averages, were moderately correlated with SAT scores, and were uncorrelated with scores related to critical-thinking dispositions. The evidence suggests that nursing programs may need to reconsider how critical thinking should be measured and evaluated.

Adult↗

PubMedDate not supplied

Assessing antipsychotic effectiveness in dementia with the factor structure of the Psychogeriatric Dependency Rating Scale (PGDRS).

OBJECTIVE: Behavioral and psychological symptoms of dementia (BPSD) impact patient functioning, caregiver burden, and transition to structured living environments. The purpose of this study was to use the derived factor structure of the Psychogeriatric Dependency Rating Scale (PGDRS) to retrospectively assess short-term antipsychotic effectiveness. SETTING AND MEASUREMENT: A principal components factor analysis was conducted with PGDRS admission ratings for a large national sample of hospitalized dementia patients (N = 2747). Changes in calculated factor scores (admission to discharge) were used to compare effectiveness for a subset of patients treated with one of three antipsychotic agents: haloperidol, olanzapine, or risperidone. RESULTS: A four-factor solution accounted for almost 60% of rating variance. Factors were interpreted as disruptive overactivity, thought/communication disorder, interpersonal aggressiveness, and destructiveness. Medication effects (adjusting for group differences) were found for only the Interpersonal Aggressiveness factor. Improvement in this factor score was significantly greater in the olanzapine group. CONCLUSIONS: Findings suggest that these four PGDRS factors can provide a useful framework for symptom assessment and for targeted treatment.

Aged↗

PubMed1999

A class of permutation tests for stratified survival data.

We propose a class of permutation tests for stratified survival data. The tests are derived using the framework of Fay and Shih (1998, Journal of the American Statistical Association 93, 387-396), which creates tests by permuting scores based on a functional of estimated distribution functions. Here the estimated distribution function for each possibly right-, left-, or interval-censored observation is based on a shrinkage estimator similar to the nonparametric empirical estimator of Ghosh, Lahiri, and Tiwari (1989, Communications in Statistics--Theory and Methods 18, 121-146), and permutation is carried out within strata. The proposed test with a weighted Mann-Whitney functional is similar to the permutation form of the stratified log-rank test when there is a large strata effect or the sample size in each stratum is large and is similar to the permutation form of the ordinary log-rank test when there is little strata effect. Thus, the proposed test unifies the advantages of both the stratified and ordinary log-rank tests. By changing the functional, we may obtain a stratified Prentice-Wilcoxon test or a difference in means test with similar unifying properties. We show through simulations the advantage of the proposed test over existing tests for uncensored and right-censored data.

AIDS-Related Opportunistic Infections↗

PubMed2001

Users in the driving seat or sitting alongside map-reading?

The government agenda is clear. At the highest level users are involved in policy making. We as service providers need to show evidence that users views are elicited and used to improve the quality of care. The tool bag of techniques used to elicit users views will be explored--questionnaires, structured interviews, focus groups and innovative cognitive techniques such as perception score cards. We explore the continuum of user-led qualitative techniques to provider-led quantitative approaches. Building a framework of techniques which cover the diverse needs of people using a speech and language therapy (SLT) service is a challenge. A greater challenge is using the views of users to bring about meaningful change.

Humans↗

PubMed1993

[The relation of ideal self to perception of self and others].

One hundred and twelve (112) junior high school students made ratings of their ideal and actual selves, and of other persons of same sex whom they liked or disliked, using uni-polar scales of 42 positive and 42 negative traits words. Positive and negative ideal-self rating scores correlated with those for actual-self and others. At the same time, rating scores on important traits for each subject which gained the highest score in ideal-self rating differed among the actual self and the liked other and disliked other--the liked other was rated more positively than the disliked other, though self-esteem affected relative positiveness of actual self to liked or disliked others. However, no such differences were found on unimportant traits which gained lower scores in ideal-self rating. These results seem to indicate that both positive and negative ideal selves provide cognitive framework for perception of self and others.

Adolescent↗

PubMed1992

Preoperative cardiac risk assessment for patients having peripheral vascular surgery.

PURPOSE: To review the methods used for preoperative cardiac risk stratification of patients having peripheral vascular surgery. DATA SOURCES: Relevant studies published before August 1991 were identified using a MEDLINE search of the English-language literature, followed by a manual search of the references of all identified articles. STUDY SELECTION: All clinical studies evaluating methods used for preoperative cardiac risk stratification of patients having peripheral vascular surgery. DATA EXTRACTION: The key data extracted from each article included the inclusion and exclusion criteria of the study patients, the techniques used for testing and the corresponding definitions of positive test results, and the clinical outcomes of the tested patients. Data were analyzed using a Bayesian conceptual framework, and pretest probabilities were converted to post-test probabilities using calculation of likelihood ratios. RESULTS: Patients with high scores on clinical cardiac risk indexes (Goldman index greater than 12 or Detsky index greater than 15), or more than three of the criteria identified by Eagle (age greater than 70 years, diabetes, angina, Q waves on electrocardiogram, or ventricular arrhythmias) are likely to be at higher risk for cardiac death and myocardial infarction after vascular surgery. Those with both low scores and none of Eagle's criteria may be at lower risk, but this result has not been reproduced by independent studies. Neither group of patients would benefit from further investigation for cardiac risk stratification. Patients with one or two of these criteria may be at intermediate risk and would benefit most from further testing for the purposes of risk stratification. Most of the published evidence shows that the absence of redistribution on dipyridamole-thallium scanning identifies a low risk for postoperative cardiac complications, whereas the presence of redistribution predicts a high risk. Preliminary reports suggest that preoperative monitoring for silent myocardial ischemia may also be useful in identifying a high-risk subset of patients. CONCLUSIONS: Patients identified clinically to be at either very low or high risk for cardiac complications after peripheral vascular surgery are unlikely to benefit from further risk stratification. Dipyridamole-thallium scanning is the test of choice for further evaluation of patients at intermediate clinical risk because studies have shown that it is sensitive enough to rule out a high-risk status for patients who do not have redistribution.

Bayes Theorem↗

PubMedDate not supplied

The FLACC: a behavioral scale for scoring postoperative pain in young children.

PURPOSE: To evaluate the reliability and validity of the FLACC Pain Assessment Tool which incorporates five categories of pain behaviors: facial expression; leg movement; activity; cry; and consolability. METHOD: Eighty-nine children aged 2 months to 7 years, (3.0 +/- 2.0 yrs.) who had undergone a variety of surgical procedures, were observed in the Post Anesthesia Care Unit (PACU). The study consisted of: 1) measuring interrater reliability; 2) testing validity by measuring changes in FLACC scores in response to administration of analgesics; and 3) comparing FLACC scores to other pain ratings. FINDINGS: The FLACC tool was found to have high interrater reliability. Preliminary evidence of validity was provided by the significant decrease in FLACC scores related to administration of analgesics. Validity was also supported by the correlation with scores assigned by the Objective Pain Scale (OPS) and nurses' global ratings of pain. CONCLUSIONS: The FLACC provides a simple framework for quantifying pain behaviors in children who may not be able to verbalize the presence or severity of pain. Our preliminary data indicates the FLACC pain assessment tool is valid and reliable.

Child↗

PubMed2025

Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction.

MOTIVATION: Single-cell Hi-C (scHi-C) data provide critical insights into chromatin interactions at individual cell levels, uncovering unique genomic 3D structures. However, scHi-C datasets are characterized by sparsity and noise, complicating efforts to accurately reconstruct high-resolution chromosomal structures. In this study, we present ScUnicorn, a novel blind super-resolution framework for scHi-C data enhancement. ScUnicorn uses an iterative degradation kernel optimization process, unlike traditional super-resolution approaches, which rely on downsampling, predefined degradation ratios, or constant assumptions about the input data to reconstruct high-resolution interaction matrices. Hence, our approach more reliably preserves critical biological patterns and minimizes noise. Additionally, we propose 3DUnicorn, a maximum likelihood algorithm that leverages the enhanced scHi-C data to infer precise 3D chromosomal structures. RESULTS: Our evaluation demonstrates that ScUnicorn achieves superior performance over the state-of-the-art methods in terms of Peak Signal-to-Noise Ratio, Structural Similarity Index Measure, and GenomeDisco scores. Moreover, 3DUnicorn's reconstructed structures align closely with experimental 3D-FISH data, underscoring its biological relevance. Together, ScUnicorn and 3DUnicorn provide a robust framework for advancing genomic research by enhancing scHi-C data fidelity and enabling accurate 3D genome structure reconstruction. AVAILABILITY AND IMPLEMENTATION: Unicorn implementation is publicly accessible at https://github.com/OluwadareLab/Unicorn.

Single-Cell Analysis↗

PubMed2000

Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths.

MOTIVATION: DNA structure plays an important role in a variety of biological processes. Different di- and tri-nucleotide scales have been proposed to capture various aspects of DNA structure including base stacking energy, propeller twist angle, protein deformability, bendability, and position preference. Yet, a general framework for the computational analysis and prediction of DNA structure is still lacking. Such a framework should in particular address the following issues: (1) construction of sequences with extremal properties; (2) quantitative evaluation of sequences with respect to a given genomic background; (3) automatic extraction of extremal sequences and profiles from genomic databases; (4) distribution and asymptotic behavior as the length N of the sequences increases; and (5) complete analysis of correlations between scales. RESULTS: We develop a general framework for sequence analysis based on additive scales, structural or other, that addresses all these issues. We show how to construct extremal sequences and calibrate scores for automatic genomic and database extraction. We show that distributions rapidly converge to normality as Nincreases. Pairwise correlations between scales depend both on background distribution and sequence length and rapidly converge to an analytically predictable asymptotic value. For di- and tri-nucleotide scales, normal behavior and asymptotic correlation values are attained over a characteristic window length of about 10-15 bp. With a uniform background distribution, pairwise correlations between empirically-derived scales remain relatively small and roughly constant at all lengths, except for propeller twist and protein deformability which are positively correlated. There is a positive (resp. negative) correlation between dinucleotide base stacking (resp. propeller twist and protein deformability) and AT-content that increases in magnitude with length. The framework is applied to the analysis of various DNA tandem repeats. We derive exact expressions for counting the number of repeat unit classes at all lengths. Tandem repeats are likely to result from a variety of different mechanisms, a fraction of which is likely to depend on profiles characterized by extreme structural features.

Animals↗

PubMed2026

Symptom assessment and health-related quality of life in children with lower urinary tract dysfunction: A retrospective cross-sectional study.

INTRODUCTION: Lower urinary tract dysfunction (LUTD) significantly impacts children's health-related quality of life (HRQoL), but key determinants of this impairment remain incompletely understood within a patient-centered framework. METHODS: This retrospective cross-sectional study enrolled 272 children with LUTD. Clinical symptoms were assessed using the Dysfunctional Voiding Scoring System (DVSS) and the Overactive Bladder Symptom Score (OABSS), and HRQoL via the Pediatric Quality of Life Inventory (PedsQL™) 4.0 Generic Core Scales. RESULTS: The mean total PedsQL score was 83.66 ± 16.07, with the School Functioning domain being the most impaired (73.75 ± 20.94). Univariate analysis identified older age (≥11 years), daytime urinary leakage, overactive bladder (OAB) symptoms, and abnormal DVSS scores as factors associated with reduced HRQoL (all P < 0.05); multivariate regression further confirmed only older age and abnormal DVSS were independent influencing factors (both P < 0.001). A significant negative correlation existed between the total DVSS score and the total PedsQL score (r = -0.390, P < 0.01), indicating that greater symptom severity predicts poorer overall HRQoL. CONCLUSION: This study indicates that in children with LUTD, the severity of voiding dysfunction (quantified by DVSS) is inversely correlated with HRQoL. Voiding dysfunction impairs multiple domains of daily functioning, including physical well-being, emotional adjustment, social interaction, and school performance. Shifting from a symptom-focused to a patient-centered care model and integrating routine HRQoL assessment into standard clinical management can optimize clinical practice for pediatric LUTD.

Humans↗

PubMed1998

Testing for differences in multiple quality of life dimensions: generating hypotheses from the experience of hospital staff.

In clinical trials with a quality of life (QoL) component, it is usual to monitor several QoL dimensions at several points in time. Multiple significance tests without formal hypotheses are problematic. It is not always feasible to specify a priori hypotheses for all variables. Can such studies be used to generate hypotheses for testing in later research only? We developed a method which can allow for formal hypothesis testing on a data set collected without a priori hypotheses in the protocol. We surveyed experienced physicians and nurses treating patients, to obtain independent expectations about differences in QoL dimensions. These 'staff expectations' will be used in the analysis of QoL data collected from breast cancer patients taking part in three randomized trials of adjuvant therapy. We propose frameworks for the informal and formal use of the experience of the staff in testing for group differences in patients' QoL scores. The method described here is anticipated to be useful for QoL studies in general, even when a priori hypotheses were specified before the studies were initiated.

Bayes Theorem↗

PubMed2026

Beyond Exons: Linking Noncoding Heritability and Polygenicity across Complex Human Traits and Disorders.

The genetic architecture of complex traits spans a continuum of polygenicity, yet it remains unclear how differences in polygenicity relate to the functional localization of SNP heritability across the genome. We use a MiXeR-based framework to partition heritability across exonic, intronic, and intergenic regions for 34 traits and introduce a likelihood-based annotation contribution score that quantifies annotation-specific impact on heritability. Exons explain a minority of heritability, and their contribution decreases with increasing polygenicity, from an average of 22% in less polygenic somatic diseases and biomarkers to 13% in highly polygenic psychiatric and cognitive phenotypes. Intergenic fractions show the opposite trend, whereas intronic fractions remain relatively stable. Analysis of a broader set of functional annotations reveals systematic differences along the polygenicity axis: highly polygenic traits show stronger contributions from comparative genomics and variant-effect scores, whereas less polygenic traits show stronger contributions in promoter, transcription, and chromatin annotations. Together, these results indicate that the functional partitioning of heritability systematically varies with polygenicity, pointing to a shift from gene-proximal regulatory architectures to architectures shaped by numerous dispersed regulatory effects as a key determinant of differences in polygenicity across traits.

Journal Article↗

PubMed1991

Nonparametric tests of association between survival time and continuously measured covariates: the logit-rank and associated procedures.

O'Brien's logit-rank procedure (1978, Biometrics 34, 243-250) is shown to arise as a score test based on the partial likelihood for a proportional hazards model provided the covariate structure is suitably defined. Within this framework the asymptotic properties claimed by O'Brien can be readily deduced and can be seen to be valid under a more general model of censoring than that considered in his paper. More important, perhaps, it is now possible to make a more natural and interpretable generalization to the multiple regression problem than that suggested by O'Brien as a means of accounting for the effects of nuisance covariates. This can be achieved either by modelling or stratification. The proportional hazards framework is also helpful in that it enables us to recognize the logit-rank procedure as being one member of a class of contending procedures. One consequence of this is that the relative efficiencies of any two procedures can be readily evaluated using the results of Lagakos (1988, Biometrika 75, 156-160). Our own evaluations suggest that, for non-time-dependent covariates, a simplification of the logit-rank procedure, leading to considerable reduction in computational complexity, is to be preferred to the procedure originally outlined by O'Brien.

Biometry↗

PubMed1986

Recognition and frequency judgments in young and elderly adults.

Three experiments examined frequency judgments and recognition memory in young and elderly adults. Subjects were presented a long list of words at either a 5-s rate (Experiments 1 & 3) or a 1-s rate (Experiment 2), after which frequency-judgment and recognition memory tasks were administered. Either an absolute (Experiments 1 & 2) or a relative (Experiment 3) frequency-judgment task was used. The recognition test, which involved repeated tests of some items, involved either one incorrect item paired with each correct item (Experiments 1 & 2), or four incorrect items (Experiment 3). Age-related differences in frequency judgments, for the more frequently presented items, were found in all three experiments. For the recognition scores, the predicted interaction between age and successive tests was found only in Experiment 3. The results were interpreted within the framework of age-related differences in elaborative encoding and in distractibility to irrelevant stimuli.

Adolescent↗